Variant report

Variant	rs4858800
Chromosome Location	chr3:48755820-48755821
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:48753231..48756384-chr3:49043125..49045455,4	K562	blood:
2	chr3:48754698..48757669-chr3:48775875..48778896,4	K562	blood:
3	chr3:48755633..48757669-chr3:48777396..48780297,2	K562	blood:
4	chr3:48716233..48718830-chr3:48753340..48756269,2	K562	blood:
5	chr3:48754717..48757980-chr3:48775781..48778989,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000178252	Chromatin interaction
ENSG00000068745	Chromatin interaction
ENSG00000213672	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 30 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10865953	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12632533	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap]
rs14018	1.00[CEU][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs4858799	0.98[EUR][1000 genomes]
rs4858830	1.00[CEU][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4974088	1.00[CEU][hapmap];0.80[TSI][hapmap]
rs6442129	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6442131	0.83[EUR][1000 genomes]
rs6766238	1.00[CEU][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs6796790	1.00[CEU][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs6801211	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs6806356	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7610519	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7621226	1.00[CEU][hapmap]
rs7639370	0.81[EUR][1000 genomes]
rs7641050	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9284885	1.00[CEU][hapmap];0.82[MEX][hapmap];0.80[TSI][hapmap]
rs9311431	1.00[CEU][hapmap]
rs9822485	0.81[LWK][hapmap];1.00[YRI][hapmap]
rs9848268	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9859473	1.00[CEU][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs9873227	0.85[EUR][1000 genomes]
rs9874010	1.00[YRI][hapmap]
rs9879978	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs9882443	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs990211	0.82[CEU][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.81[MEX][hapmap];0.89[MKK][hapmap];0.92[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv590247	chr3:48661985-48801929	Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:30)

SNP	Gene	Cis/trans	Tissue	Source
rs4858800	DALRD3	cis	cerebellum	SCAN
rs4858800	ARIH2	Cis_1M	lymphoblastoid	RTeQTL
rs4858800	NCKIPSD	cis	cerebellum	SCAN
rs4858800	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs4858800	NICN1	cis	parietal	SCAN
rs4858800	ZNF589	cis	parietal	SCAN
rs4858800	WDR6	cis	parietal	SCAN
rs4858800	AMT	cis	cerebellum	SCAN
rs4858800	LEPR	trans	lymphoblastoid	RTeQTL
rs4858800	DALRD3	cis	parietal	SCAN
rs4858800	AMT	cis	Thyroid	GTEx
rs4858800	NICN1	cis	Thyroid	GTEx
rs4858800	QARS	cis	parietal	SCAN
rs4858800	NICN1-AS1	cis	Thyroid	GTEx
rs4858800	NCKIPSD	cis	Nerve Tibial	GTEx
rs4858800	AMT	cis	Artery Tibial	GTEx
rs4858800	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs4858800	TLR9	cis	parietal	SCAN
rs4858800	WDR6	cis	cerebellum	SCAN
rs4858800	QRICH1	cis	cerebellum	SCAN
rs4858800	NICN1	cis	cerebellum	SCAN
rs4858800	NCKIPSD	cis	Muscle Skeletal	GTEx
rs4858800	CDC25A	cis	cerebellum	SCAN
rs4858800	WDR6	cis	Muscle Skeletal	GTEx
rs4858800	PHF7	cis	parietal	SCAN
rs4858800	AMT	cis	parietal	SCAN
rs4858800	AMT	cis	Adipose Subcutaneous	GTEx
rs4858800	AMT	cis	lung	GTEx
rs4858800	P4HTM	cis	parietal	SCAN
rs4858800	IQCF1	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48754800-48759000	Weak transcription	Gastric	stomach
2	chr3:48755200-48756000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr3:48755200-48756000	Enhancers	Pancreas	Pancrea
4	chr3:48755200-48757600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr3:48755200-48758000	Weak transcription	Fetal Lung	lung
6	chr3:48755200-48759000	Weak transcription	Fetal Kidney	kidney
7	chr3:48755200-48760000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr3:48755200-48760200	Weak transcription	Small Intestine	intestine
9	chr3:48755400-48756000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr3:48755400-48756000	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr3:48755400-48756200	Enhancers	HepG2	liver
12	chr3:48755400-48756800	Weak transcription	Fetal Intestine Small	intestine
13	chr3:48755400-48757600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr3:48755400-48757600	Weak transcription	Spleen	Spleen
15	chr3:48755400-48758000	Weak transcription	Fetal Intestine Large	intestine
16	chr3:48755400-48758000	Weak transcription	Stomach Mucosa	stomach
17	chr3:48755400-48759000	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr3:48755400-48760200	Weak transcription	Colonic Mucosa	Colon
19	chr3:48755400-48760200	Weak transcription	A549	lung
20	chr3:48755400-48760400	Weak transcription	Duodenum Mucosa	Duodenum
21	chr3:48755600-48760200	Weak transcription	K562	blood
22	chr3:48755800-48756800	Enhancers	Rectal Mucosa Donor 29	rectum

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